Those that I've seen have generally been some kind of custom application (most I've seen are written in .NET using C/VB) that basically communicates with a server and pulls files from the server if they're newer or don't match the server version.
I'm sure there's probably some customizable commercial software out there to do basically the same thing as well. I've never looked in to auto-updaters in general very deeply as I don't particularly care for them, although they do seem to be popular as kind of "set it and forget it" programs that don't require too much tinkering once the user has them installed/configured the first time.
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